In all honesty, if this is the case, why does the Galaxy S3 also have incredible battery life with essentially the exact same internals as the E4GLTE?
Indeed. I do not believe it has anything to do with battery life. Except for rogue or "bad" apps, true multitasking will not use much more battery than this strange HTC configuration. Apps that don't need to do anything in the background (the overwhelming majority) will sleep. Apps that do need to do something WILL use some battery, but that is usually what the user would want, anyway.
Yes, this strange HTC configuration COULD offer a degree of "protection" against bad or rogue apps... but the cost of doing so is extremely high. In any case, it is still totally unacceptable to ruin the core operational behavior of Android and not even make it optional to undo (through some option in Settings).